HIV/AIDS treatment is costly. Lesotho as a resource–limited country depends mostly on donor funding for HIV/AIDS treatment and care. Knowledge of how much was spent on treatment of HIV/AIDS was lacking. This leads to overstocking of some ART medicines resulting in expiry. Sufficient funds need to be secured for the treatment programme. The main objective of the study is to assess the cost of antiretroviral medication treatments, by specifically assessing the cost of antiretroviral regimens, antiretroviral side effects, and the cost of medicines used for prophylaxis and treatment of opportunistic infections as well as the cost of monitoring laboratory tests and dietary supplements. The study engaged both public and private ART clinics in the Maseru District in Lesotho. The study population consisted of 1 424 patients and study period was between 12 and 56 months from January 2004 to August 2008. Retrospective observational method was used. The cost for HIV/AIDS treatment comprised the cost of antiretroviral medicines and those used for their side effects, opportunistic infections (OI) prophylaxis and treatment, dietary supplements as well as monitoring laboratory tests. Prescribed daily dose (PDD) was used to calculate the cost of all the medicines used. To determine significant differences in average costs for various regimens d– values were used, while a cost/prevalence index was used to determine whether the cost was worth spending on the population or not. Cost–effectiveness ratio was also utilized in order to assess whether the cost born was worth the benefit. The main findings revealed that regimens 1a (stavudine/lamivudine/nevirapine) and 1c (zidovudine/lamivudine/nevirapine) were the least expensive (cost/prevalence index of 0.6 and 0.7 respectively). Regimens containing efavirenz were found to be more expensive than those containing nevirapine (cost/prevalence index of 1.2 and 1.7 respectively). When using d–values, there was a significant difference between the cost of regimens 1a and 1b, 1a and 1d, 1c and 1d and the information could be used for regimen switching decisions. Increase in CD4 cell count was more in stavudine–based regimens than in zidovudine–based regimens, which cost less per treatment. Cost effectiveness ratio was lower in 1a with R9.42/1cell/mm3 of CD4 cell count increase, and the highest was 1d with R31.77/1cell/mm3 of CD4 cell count increase. Therefore it was concluded that stavudine–based regimens are less costly as they have the lowest cost– effectiveness ratio in the Lesotho clinic environment.